The 2025 In Vitro Biology Meeting in Norfolk, Virginia featured the Bob V. Conger Plant Biotechnology Student Oral Presentation Competition for Plant Biotechnology students. This competition is named in honor of the legacy of the late Bob V. Conger, and the fund appropriated for this competition is dedicated to recognizing quality student oral presentations at the SIVB annual meetings. Presenters were evaluated on experimental design, data analysis, proper interpretation of results, originality of the study, technical difficulty, and presentation skills. Our expert panel of judges consisted of Ritesh Kumar (Boyce Thompson Institute, USA), Qingzhen Jiang (Boyce Thompson Institute, USA), Arjun Ojha Kshetry (Texas Tech University, USA), and Muruganantham (Murug) Mookkan (Plastomics Inc., USA). We selected six student finalists, each demonstrating knowledge and dedication to their research areas. The judges recognized Joshua S. Clem (University of Maryland, USA) with the 1st place award, Yeyen Novitasari (University of Florida, USA) with the 2nd place award, and Khushbu Kumari (Institute of Himalayan Bioresoruce Technology, India) with the 3rd place award. The winners were presented with a certificate and a cash award. We encourage all plant biotechnology students to take advantage of this opportunity to compete in future competitions and develop their oral presentation skills.
Submitted by Muruganantham (Murug) Mookkan
First Place
A Novel Type I-F CRISPR System Confers Kilobase-scale Genomic Deletions at GC-rich PAMs in Plants
Joshua Clem
CRISPR-Cas systems have provided remarkably capable tools for editing plant genomes. Type II and Type V CRISPR-Cas nucleases, Cas9 and Cas12a, respectively, are commonly used to generate small, site-specific indels. However, achieving large genomic deletions with high efficiency in plants remains challenging using these canonical CRISPR-Cas systems. Type I CRISPR systems, which encode the multi-effector Cascade machinery, are known to generate large-scale deletions but have received comparatively little attention for plant genome editing. Moreover, several Type I subtypes have been unexplored for use in plants, leaving untapped potential for novel variants possessing nuclease activity at alternative PAMs and enhanced editing efficiency. Aided by genome-database discovery tools, we uncover a Type I-F CRISPR system derived from Methylomonas methanica (MmeCascade). When expressed in transgenic rice plants, the MmeCascade, harboring a unique Cas3-Cas2 fusion, results in large genomic deletions on the order of several kilobases at two genomic target sites containing GC-rich PAMs. Strikingly, deletions elicited by MmeCascade are bidirectional and occur with high editing efficiency. To complement this potent genome editor, we adapt a genome editing analysis tool for compatibility with Oxford Nanopore DNA sequencing of long-range PCR amplicons, complete with target site interrogation and data visualization capabilities. Equipped with this novel Type I-F CRISPR system, engineering large-scale genomic perturbations in plants is achievable with high efficiency, enabling investigations into the functional roles of long non-coding RNAs, cis-regulatory elements, and gene clusters in plants.
Joshua Clem, Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD. Abstract Presentation: P-1006
Second Place
Optimizing Plant Regeneration and Agrobacterium-mediated Transformation in African and French Marigold Genotypes
Yeyen Novitasari
Marigolds are highly valued worldwide for their vibrant flowers and rich carotenoid content, which make them popular as natural pigments and antioxidants in food, cosmetics, and poultry feed. However, plant regeneration and transformation in marigolds are hindered by underdeveloped tissue culture techniques, leading to low transformation efficiency. This study aims to optimize plant regeneration and transformation through indirect organogenesis and to develop novel flower traits in both African and French marigolds using Agrobacterium-mediated transformation. Three genotypes from each marigold variety were tested for regeneration potential using eight combinations of callus induction media (CIM) and two combinations of shoot induction media (SIM). The best genotypes for plant regeneration were ‘Marvel II Yellow’ and ‘Bonanza Yellow,’ with the optimal regeneration media comprising 0.5 mg/l NAA and 2.5 mg/l BAP for CIM, and 0.1 mg/l NAA and 1 mg/l BAP for SIM. These genotypes were then used to develop novel flower colors through the overexpression of the RUBY, ROSEA, and DELILA genes. Cotyledons were used as explants for both regeneration and transformation, with the ideal explant age found to be 4–5 days. Novel flower colors were successfully obtained in African marigolds, including reddish-yellow and pinkish-yellow flowers in ‘Marvel II Yellow’ with RUBY, purplish-yellow flowers in ‘Marvel II Yellow’ with DELILA, and reddish-yellow and purplish-yellow flowers in ‘Bonanza Yellow’ with RUBY and ROSEA, respectively. These results underscore the importance of this study in advancing the development of novel traits in marigolds through biotechnology.
Yeyen Novitasari, Department of Environmental Horticulture, University of Florida, Gainesville, FL; Mid-Florida Research and Education Center, University of Florida, Apopka, FL; and Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Bogor 16911, INDONESIA. Abstract Presentation: P-1008
Third Place
Integrating Artificial Intelligence and Multi-omics for Precision Organogenesis, Embryogenesis and Secondary Metabolite Production in Ferula assa-foetida L.
Khushbu Kumari
In commercial-scale in vitro propagation, artificial intelligence techniques has emerged as a highly valuable tool for automated somatic embryo analysis. Ferula assa-foetida, a commercially significant spice and medicinal plant, requires optimized regeneration systems for propagation, conservation, and genetic engineering. Current study established a standardized protocol for in direct organogenesis via somatic embryogenesisin F. assa-foetida, identifying globular, heart, torpedo, and cotyledonary stages. Machine learning (ML) approaches, including convolutional neural networks (CNNs) and Random Forest (RF), were utilized to optimize shoot induction and proliferation, with CNNs showing superior predictive accuracy. Additionally, transcriptome, proteome and metabolome analysis shed light on the cellular reprogramming involved duringin vitro organogenesis. LC- MS analysis revealed significant role of secondary metabolite dynamics during organogenesis, which highlighted the roles of phytohormones and phytoconstituents. Similarly, RNA-seq analysis and protein profiling during different developmental stages revealed various key transcription factors including Somatic Embryogenesis Receptor-like Kinase (SERK), Wuschel (WUS), Scarecrow (SCR), and Cup-Shaped Cotyledon (CUC), terpene synthase (TPS), 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) and pathways involved in cellular reprogramming and developmental transitions. These genes regulate phytohormone biosynthesis, transport, and signaling pathways. The study uncovered the molecular interplay between secondary metabolite biosynthesis and cellular dynamics during organogenesis. Our findings deepen our understanding of automated, large-scale propagation systems, improving regeneration protocols and enabling advanced functional studies. This research forms the basis for commercial applications, genetic enhancement, and conservation efforts for F. assa-foetida.
Khushbu Kumari, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT). Palampur, Himachal Pradesh, INDIA and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, INDIA. Abstract Presentation: P-1009
